Package: DeeDeeExperiment
Title: DeeDeeExperiment: An S4 Class for managing and exploring omics
        analysis results
Version: 1.2.0
Authors@R: 
    c(
        person(
            given = "Najla", family = "Abassi", role = c("aut", "cre"), 
            email = "abassi.nejla96@gmail.com",
            comment = c(ORCID = "0000-0001-8357-0938")
        ),
        person(
            given = "Lea", family = "Schwarz", role = c("aut"),
            email = "lea.schwarz@uni-mainz.de",
            comment = c(ORCID = "0000-0003-2554-0583")
        ),
        person(
            given = "Federico", family = "Marini", role = c("aut"), 
            email = "marinif@uni-mainz.de",
            comment = c(ORCID = "0000-0003-3252-7758")
        )
    )
Description: DeeDeeExperiment is an S4 class extending the
        SingleCellExperiment class, designed to integrate and manage
        omics analysis results. It introduces two dedicated slots to
        store Differential Expression Analysis (DEA) results and
        Functional Enrichment Analysis (FEA) results, providing a
        structured approach for downstream analysis.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.5.0), SingleCellExperiment
Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2,
        edgeR, limma, writexl, cli
Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db,
        topGO, clusterProfiler, DEFormats, ExperimentHub, scater,
        muscat, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/imbeimainz/DeeDeeExperiment
BugReports: https://github.com/imbeimainz/DeeDeeExperiment/issues
biocViews: Software, Infrastructure, DataRepresentation,
        GeneExpression, Transcription, Transcriptomics,
        DifferentialExpression, Pathways, GO
Config/testthat/edition: 3
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:05:18 UTC
RemoteUrl: https://github.com/bioc/DeeDeeExperiment
RemoteRef: RELEASE_3_23
RemoteSha: b29a2a976608578b80acb289c6266763dc843c8a
NeedsCompilation: no
Packaged: 2026-04-29 20:59:51 UTC; root
Author: Najla Abassi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8357-0938>),
  Lea Schwarz [aut] (ORCID: <https://orcid.org/0000-0003-2554-0583>),
  Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Najla Abassi <abassi.nejla96@gmail.com>
Built: R 4.6.0; ; 2026-04-30 10:08:59 UTC; windows
